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Currently my workflow to update to a new CM nightly and reinstall my custom kernel is this:

  1. Install the CM update using the CM updater
  2. Boot into recovery manually and install the zip file containing the kernel.

I wonder if there's a way to do this in one go.

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This is indeed possible by downloading the ZIP file for the new version (e.g. using the CM updater without installing it after downloading it).

Afterwards the device needs to be rebooted into Recovery. The CM update zip can be found in the cmupdater folder on the sd card (when downloaded using the updater) and installed using the "install zip" option (in CWM, might be named differently in TWRP).

When the CM zip is installed, the kernel zip can be installed using the same method.

While a data wipe is usually not necessary, it is a good idea to wipe both cache and dalvik cache before rebooting.

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